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Old 08-16-2010, 03:32 PM   #21
dukevn
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Anybody knows how I can trim out the adapter sequence with a certain number of mismatch (1 or 2)?

Thanks,

D.
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Old 08-17-2010, 01:32 AM   #22
didymos
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Hi,

In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

tomek
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Old 08-17-2010, 11:52 AM   #23
dukevn
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Quote:
Originally Posted by didymos View Post
Hi,

In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

tomek
Thanks, but I want to trim the adapter sequence, not n nucleotides.
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Old 11-03-2010, 02:35 PM   #24
mgogol
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fastx_clipper can trim adapter sequence.
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Old 11-03-2010, 04:59 PM   #25
jdanderson
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Hello Everyone,

I would like to second mgogol's suggestion. It is part of a larger set of tools called FASTX Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html

I've found the tools to be very useful and user friendly.

Cheers,
Johnathon
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Old 06-27-2011, 11:07 PM   #26
zeam
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Hi everyone,
When you were processing smRNA-seq data,which software did you use?I have attempted SOAP2 and bowtie,both of them didn't work well enough,many of the reads could not map to the reference.But when I used blat,it works well except consuming time.Can you guys give me some suggestions?My data is from plants,and I want to sepate miRNA and siRNA from smRNA-seq data.
Thanks!
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Old 06-28-2011, 12:16 AM   #27
NicoBxl
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did you allow mismatches in your alignment ?
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Old 06-28-2011, 01:47 AM   #28
zeam
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Quote:
Originally Posted by NicoBxl View Post
did you allow mismatches in your alignment ?
What I want is to dissect the correlation between smRNA and DNA methylation.Previous studies reveals that both of miRNA and siRNA involed in DNA methylation.The problem I met is 1)mapping;2)separating miRNA and siRNA from smRNA-seq data.Can you give me some suggestions if you have some experience on these subjects?
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Old 05-09-2013, 06:42 AM   #29
unique379
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Dear all,

as above discussions and suggestion, could i use bowtie something like this for miRNA alignment ?? just please make me sure.

bowtie --sam -q -n 0 -l 15 -e 99999 -k 200 -a --chunkmbs 1024 --best ....
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Old 06-10-2013, 06:25 AM   #30
JonB
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Quote:
Originally Posted by yjhua2110 View Post
in our deepBase database, we use options: –k 200 –v 0. the Specifying the parameters (–k 200 –v 0) instructs Bowtie to report up to 200 perfect hits for each read.

deepBase is a platform for annotating and discovering small and long ncRNAs from next generation sequencing data. It is available at http://deepbase.sysu.edu.cn
I am mapping reads from a small RNA sequencing, and I am curious how you treat the results after mapping with the -k 200 option? Do you assemble the transcripts? Or do you report all the locations where a read has been mapped?

Last edited by JonB; 06-10-2013 at 06:26 AM. Reason: lacked quote
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Old 06-10-2013, 07:05 AM   #31
sBeier
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Usually, with small RNAs being not bigger than 24 nt, you would filter for reads between maybe 15 - 28 nt length. Those are the complete transcripts, so no need for any assembly.
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Old 06-10-2013, 10:44 AM   #32
JonB
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Could you run a program like Cufflinks specifying a mean transcript length of about 18 nts, and then get a gtf file of the different transcripts?
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